DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Statistical and machine learning approaches to predicting protein–ligand interactions

(2018) Lucy J Colwell   CURRENT OPINION IN STRUCTURAL BIOLOGY

Drug-Target Interactions: Prediction Methods and Applications

(2018) Shanmugam Anusuya et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark

(2018) Yan Li et al.   Nature Protocols

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

(2016) Xing Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MOLS 2.0: software package for peptide modeling and protein–ligand docking

(2016) D. Sam Paul et al.   JOURNAL OF MOLECULAR MODELING

Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations

(2015) Priyashree Chaudhary et al.   BIOINFORMATICS

Deep learning

(2015) Yann LeCun et al.   NATURE

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Complex diseases require complex therapies

(2013) Ravi Iyengar   EMBO REPORTS

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

(2013) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Mechanisms and insights into drug resistance in cancer

(2013) Hiba Zahreddine et al.   Frontiers in Pharmacology

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery

(2012) B Jayaram et al.   BMC BIOINFORMATICS

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY